Query 028909
Match_columns 202
No_of_seqs 119 out of 329
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 04:27:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028909.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028909hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2536 MAM33, mitochondrial m 100.0 2.5E-45 5.4E-50 307.9 19.3 181 13-201 56-263 (263)
2 PF02330 MAM33: Mitochondrial 100.0 6E-42 1.3E-46 283.8 12.6 167 24-199 1-204 (204)
3 KOG4024 Complement component 1 100.0 9.4E-31 2E-35 214.4 21.0 182 13-202 66-266 (266)
4 TIGR01881 cas_Cmr5 CRISPR-asso 80.6 6.3 0.00014 30.4 6.1 43 154-196 70-121 (127)
5 PF08513 LisH: LisH; InterPro 73.2 7 0.00015 21.7 3.3 25 153-177 1-25 (27)
6 PF00123 Hormone_2: Peptide ho 67.6 12 0.00026 21.2 3.5 24 170-193 4-27 (28)
7 KOG4233 DNA-bridging protein B 63.9 11 0.00024 26.8 3.5 36 160-195 32-67 (90)
8 PF10929 DUF2811: Protein of u 55.5 12 0.00025 25.0 2.2 31 149-179 4-41 (57)
9 PF09862 DUF2089: Protein of u 52.4 24 0.00051 26.8 3.8 54 122-176 6-59 (113)
10 PRK11814 cysteine desulfurase 52.1 29 0.00064 32.6 5.3 51 143-197 423-478 (486)
11 smart00070 GLUCA Glucagon like 52.1 23 0.00049 19.9 2.8 22 171-192 5-26 (27)
12 PRK13031 preprotein translocas 50.8 37 0.00081 27.0 4.8 71 46-129 17-88 (149)
13 PF02961 BAF: Barrier to autoi 50.7 20 0.00043 26.0 3.0 37 158-195 30-67 (89)
14 COG1490 Dtd D-Tyr-tRNAtyr deac 49.2 30 0.00064 27.3 4.0 56 120-175 70-125 (145)
15 PF13154 DUF3991: Protein of u 46.0 16 0.00034 25.3 1.9 17 162-178 2-19 (77)
16 PF08275 Toprim_N: DNA primase 45.0 16 0.00035 27.8 2.0 17 158-174 13-29 (128)
17 PHA01623 hypothetical protein 43.6 48 0.001 21.7 3.8 29 150-180 19-47 (56)
18 PHA02360 hypothetical protein 39.1 33 0.00071 23.4 2.5 17 153-169 29-45 (70)
19 PF00070 Pyr_redox: Pyridine n 36.6 37 0.0008 23.0 2.6 21 149-169 36-56 (80)
20 PF13434 K_oxygenase: L-lysine 36.6 23 0.0005 31.5 1.9 33 158-193 70-105 (341)
21 PF13495 Phage_int_SAM_4: Phag 36.0 83 0.0018 21.1 4.4 34 155-200 1-34 (85)
22 PF07063 DUF1338: Domain of un 34.5 78 0.0017 28.0 4.8 46 149-194 100-180 (302)
23 PF14265 DUF4355: Domain of un 33.8 96 0.0021 23.1 4.7 40 154-194 69-108 (125)
24 smart00777 Mad3_BUB1_I Mad3/BU 31.8 80 0.0017 24.2 4.0 30 157-186 83-112 (125)
25 TIGR02793 nikR nickel-responsi 31.6 1.2E+02 0.0026 23.3 4.9 20 150-169 6-25 (129)
26 smart00667 LisH Lissencephaly 30.7 75 0.0016 17.2 2.9 27 152-178 3-29 (34)
27 PF12122 DUF3582: Protein of u 29.0 54 0.0012 24.2 2.5 22 152-173 9-30 (101)
28 PF02268 TFIIA_gamma_N: Transc 28.7 1E+02 0.0023 19.8 3.5 30 150-179 10-39 (49)
29 PF10915 DUF2709: Protein of u 28.2 91 0.002 26.1 3.9 39 155-193 196-235 (238)
30 PF08321 PPP5: PPP5 TPR repeat 27.7 47 0.001 24.2 2.0 10 140-149 39-48 (95)
31 PRK04460 nickel responsive reg 27.1 1.6E+02 0.0034 22.9 4.9 20 150-169 8-27 (137)
32 PF12826 HHH_2: Helix-hairpin- 27.0 42 0.0009 22.3 1.5 41 148-188 23-63 (64)
33 COG4003 Uncharacterized protei 26.9 88 0.0019 22.6 3.2 26 158-183 52-78 (98)
34 PF13376 OmdA: Bacteriocin-pro 26.1 1.6E+02 0.0034 19.4 4.2 40 149-196 4-43 (63)
35 PF13034 DUF3895: Protein of u 25.4 1.2E+02 0.0027 21.4 3.7 28 151-178 1-30 (78)
36 TIGR01981 sufD FeS assembly pr 25.0 82 0.0018 28.3 3.4 39 142-184 314-352 (366)
37 PRK13654 magnesium-protoporphy 24.9 71 0.0015 28.8 2.9 35 141-177 67-101 (355)
38 PF01316 Arg_repressor: Argini 24.4 62 0.0014 22.2 2.0 16 156-171 22-37 (70)
39 PRK02967 nickel responsive reg 23.5 2.2E+02 0.0048 22.1 5.2 20 150-169 7-26 (139)
40 PHA01748 hypothetical protein 23.4 2.3E+02 0.0049 18.7 5.4 20 150-169 8-27 (60)
41 PF07671 DUF1601: Protein of u 23.1 1.2E+02 0.0025 18.3 2.8 17 161-177 6-22 (37)
42 PF11985 DUF3486: Protein of u 23.1 3.9E+02 0.0084 21.3 6.8 32 148-179 7-40 (180)
43 PF13794 MiaE_2: tRNA-(MS[2]IO 22.9 80 0.0017 26.0 2.7 45 156-200 52-99 (185)
44 PF01458 UPF0051: Uncharacteri 22.8 49 0.0011 27.4 1.5 34 141-178 193-226 (229)
45 PF10281 Ish1: Putative stress 22.3 73 0.0016 18.8 1.8 15 157-171 7-21 (38)
46 PF08311 Mad3_BUB1_I: Mad3/BUB 21.9 94 0.002 23.5 2.8 30 157-186 83-112 (126)
47 COG3486 IucD Lysine/ornithine 21.3 72 0.0016 29.6 2.3 36 158-193 73-108 (436)
48 CHL00185 ycf59 magnesium-proto 21.2 85 0.0018 28.3 2.6 34 142-177 64-97 (351)
49 TIGR02029 AcsF magnesium-proto 20.7 87 0.0019 28.1 2.6 30 147-177 62-91 (337)
50 PF08812 YtxC: YtxC-like famil 20.5 1.7E+02 0.0037 24.5 4.3 26 172-200 105-130 (221)
51 TIGR01446 DnaD_dom DnaD and ph 20.5 2.7E+02 0.0058 18.4 4.6 34 150-183 12-45 (73)
52 PF09701 Cas_Cmr5: CRISPR-asso 20.5 1.5E+02 0.0032 22.2 3.6 41 155-195 66-117 (122)
53 PRK10948 cysteine desulfurase 20.2 1.2E+02 0.0025 28.1 3.5 38 143-184 360-397 (424)
54 COG0218 Predicted GTPase [Gene 20.2 1.5E+02 0.0033 24.7 3.8 37 124-166 66-104 (200)
55 cd06206 bifunctional_CYPOR The 20.0 97 0.0021 27.8 2.9 41 153-193 79-120 (384)
56 PF12123 Amidase02_C: N-acetyl 20.0 1.2E+02 0.0025 19.2 2.4 20 149-168 22-41 (45)
No 1
>KOG2536 consensus MAM33, mitochondrial matrix glycoprotein [Energy production and conversion]
Probab=100.00 E-value=2.5e-45 Score=307.88 Aligned_cols=181 Identities=27% Similarity=0.391 Sum_probs=149.3
Q ss_pred cchhhHHHHHHHHHHHHHHHhcCCCCC----CCCCCCCCceEeecCCCCceEEEEeecCCCceEEEEEeeC-----C--C
Q 028909 13 KALQDLNLLKILNSEITHELSSNRFQD----NQSGTLGDFKVEYDAPQSHDVVLRTKFESGEEVAVSALLG-----P--E 81 (202)
Q Consensus 13 ~~~~d~~L~~~L~~EI~~E~~~~~~~~----~~~~~~~~F~i~~d~~g~~~v~L~r~~~~~E~I~V~~~~~-----~--~ 81 (202)
+++.++.|++++.+||+++++..++.. ..+....+|.++ |.||.++|+|+|+|+ ||+|+|++.|. + +
T Consensus 56 rss~t~~~~r~i~~EI~s~~~~~~~~~~~~~~~~~~~~pf~ie-d~PG~q~V~L~r~~~-GE~i~V~v~v~~~~~~~~~e 133 (263)
T KOG2536|consen 56 RSSFTQNLLRVILSEIKSEKKHDPPHQVLEEEIPLSKFPFEIE-DRPGEQWVVLTRKFE-GETIKVEVDVTQLVTDEPEE 133 (263)
T ss_pred hcccccchHHHHHHHHHHhhhcCCchhhhhhccccCCCCccee-cCCCceEEEEEeecC-CceEEEEEeeehhccCCcch
Confidence 456689999999999999988764322 123344679996 999999999999998 89999999862 1 1
Q ss_pred CCC------CCC---------CCCcceeeEEEEEcCCCCceEEEEeeecccccCCCceEEeeEEEecCCCC-CCCCCccC
Q 028909 82 TFV------RES---------RFPREVLMKVCLTKPVLCSILQFDCRVTEKHIEGSDFDIRNAYYLQSSTC-LGRPLYRG 145 (202)
Q Consensus 82 ~~~------ed~---------~~~~~~~~~V~I~K~~~~~~L~f~C~~~~~~~~~~~~~I~~v~~~~~~~~-~~~~~Y~G 145 (202)
+.+ +++ .....+.+.|+|+|++ |.+|+|.|++|||+ |.|+++++.++... ...-+|.|
T Consensus 134 ~~de~e~~~~~~~~~~~~~~~~~~~~iplvV~vsK~~-~~sLef~cta~pD~-----i~Idslsv~~~~d~~~~~l~Y~G 207 (263)
T KOG2536|consen 134 DEDETEEEDEDEDQEDDDPLSDNISNIPLVVTVSKGD-GVSLEFLCTAFPDE-----IVIDSLSVRPPIDASEDQLAYEG 207 (263)
T ss_pred hccccccccccccccccccCCCcceeeEEEEEEecCC-CceEEEEeecCCCc-----eEEeeeEecCCCCccchhhhccC
Confidence 110 110 1122478999999966 68999999999875 89999999988753 33369999
Q ss_pred CCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 028909 146 PMFSSLDPQLQVALKEYLVARGIGEHLTNYLLLHLHKKEQDQYVNWLQKLESMVAK 201 (202)
Q Consensus 146 P~f~~LDe~Lq~~~~~yLeeRGId~ela~fl~~y~~~KE~~eYi~WL~~vk~Fv~~ 201 (202)
|.|++|||+||++||.|||+|||+++|+.||++||.+|+++||++||++||+||++
T Consensus 208 P~F~eLDe~Lqd~fh~fLEeRGI~esl~~FL~~ym~~Kd~rEYl~WlksvK~Fv~~ 263 (263)
T KOG2536|consen 208 PSFEELDEELQDSFHRFLEERGIKESLASFLHAYMKNKDSREYLRWLKSVKSFVEQ 263 (263)
T ss_pred CChhHHhHHHHHHHHHHHHHcCCCHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhcC
Confidence 99999999999999999999999999999999999999999999999999999974
No 2
>PF02330 MAM33: Mitochondrial glycoprotein; InterPro: IPR003428 This mitochondrial matrix protein family contains members of the MAM33 family which bind to the globular 'heads' of C1Q.; GO: 0005759 mitochondrial matrix; PDB: 3QV0_A 1YQF_F 3JV1_A 1P32_A 3RPX_A.
Probab=100.00 E-value=6e-42 Score=283.77 Aligned_cols=167 Identities=33% Similarity=0.527 Sum_probs=129.4
Q ss_pred HHHHHHHHHhcCCCCCCCC--CCCCCceEeecCCCCceEEEEeecCCCceEEEEEeeC----CC---CCC-----CC-C-
Q 028909 24 LNSEITHELSSNRFQDNQS--GTLGDFKVEYDAPQSHDVVLRTKFESGEEVAVSALLG----PE---TFV-----RE-S- 87 (202)
Q Consensus 24 L~~EI~~E~~~~~~~~~~~--~~~~~F~i~~d~~g~~~v~L~r~~~~~E~I~V~~~~~----~~---~~~-----ed-~- 87 (202)
|++||++|++++...+... -+..+|.+. +.+|+++|+|+|+|+ +|+|+|.|+++ ++ +.+ ++ +
T Consensus 1 L~~EI~~E~~~~~~~~~~~~~l~~~~f~i~-d~~g~~~V~L~r~~~-~E~I~V~f~v~~~~~~~~~~~~~~~~~~e~~~~ 78 (204)
T PF02330_consen 1 LKSEIKYEKENYESPDSLKEFLPPSPFEIE-DKPGGSEVTLTREFG-GEKIRVTFNVNDSVDPPFDEDEDEEEGEEEEEE 78 (204)
T ss_dssp HHHHHHHHHHHCT-HHHHCCHHHHTTTCEE-EECCTTEEEEEEEET-TEEEEEEEECCCH--------------------
T ss_pred ChHHHHHHHHcccccHHHHhhCCCCCCEEE-EcCCCcEEEEEEecC-CcEEEEEEECCccCCCCCCccccchhccccccc
Confidence 7899999998774100111 134668996 899999999999998 69999999864 11 100 00 0
Q ss_pred --C-------CC-----cceeeEEEEEcCCCCceEEEEeeecccccCCCceEEeeEEEecCCCC-------CCCCCccCC
Q 028909 88 --R-------FP-----REVLMKVCLTKPVLCSILQFDCRVTEKHIEGSDFDIRNAYYLQSSTC-------LGRPLYRGP 146 (202)
Q Consensus 88 --~-------~~-----~~~~~~V~I~K~~~~~~L~f~C~~~~~~~~~~~~~I~~v~~~~~~~~-------~~~~~Y~GP 146 (202)
. .+ ..+.++|+++|++ +.|.|.|+++++ .|.|++|+++++... .....|.||
T Consensus 79 ~~~~~~fe~~~~~~~~~~~~~~~v~~~k~~--~~l~f~~~~~~d-----~~~I~~v~~~~~~~~~~~~~~~e~~~~y~gp 151 (204)
T PF02330_consen 79 EISEPDFEVEIPKEDEVSFPFFVVVISKPG--DGLEFDCSAQDD-----EFSIDNVSFYPDGDSTKDSAEAEWEDAYYGP 151 (204)
T ss_dssp ------CEEECCCCCCCEEEEEEEEEECTC--EEEEEEEECCTT-----EEEEEEEEEESSHHHH--SHHHHHHCSS-EC
T ss_pred ccccccchhcccccccccceeEEEEEEcCC--CceEEeEeccCc-----eEEEEEEEEecCccccccccchhccccccCC
Confidence 0 11 1235788999987 459999998654 499999999987542 114689999
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 028909 147 MFSSLDPQLQVALKEYLVARGIGEHLTNYLLLHLHKKEQDQYVNWLQKLESMV 199 (202)
Q Consensus 147 ~f~~LDe~Lq~~~~~yLeeRGId~ela~fl~~y~~~KE~~eYi~WL~~vk~Fv 199 (202)
.|++||++||++|++||++||||++||+||++||++|||++|++||++|++||
T Consensus 152 ~f~~LDe~Lq~~~~~yLeeRGId~~la~fl~~y~~~kEq~eYi~wL~~l~~Fv 204 (204)
T PF02330_consen 152 DFDELDENLQDAFMNYLEERGIDEELANFLHDYSTDKEQREYIRWLKNLKKFV 204 (204)
T ss_dssp EGGGSBHHHHHHHHHHHHHTT-SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccccCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 99999999999999999999999999999999999999999999999999997
No 3
>KOG4024 consensus Complement component 1, Q subcomponent binding protein/mRNA splicing factor SF2, subunit P32 [Defense mechanisms]
Probab=99.98 E-value=9.4e-31 Score=214.35 Aligned_cols=182 Identities=21% Similarity=0.293 Sum_probs=144.7
Q ss_pred cchhhHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCceEeecCCCCceEEEEeecCCCceEEEEEeeC----CC-CCCCCC
Q 028909 13 KALQDLNLLKILNSEITHELSSNRFQDNQSGTLGDFKVEYDAPQSHDVVLRTKFESGEEVAVSALLG----PE-TFVRES 87 (202)
Q Consensus 13 ~~~~d~~L~~~L~~EI~~E~~~~~~~~~~~~~~~~F~i~~d~~g~~~v~L~r~~~~~E~I~V~~~~~----~~-~~~ed~ 87 (202)
|+..++.|+++|..||+.|.++.... ..|+.+.||.++ ..+.+|.|+|+.+ +|+|.|+||++ ++ ++++++
T Consensus 66 ht~~~~alv~fl~~Ei~~erk~qkgk-t~Pkt~~Gf~v~---l~gaev~Ltkk~~-~Eki~V~FNvNhsvd~~e~~e~eP 140 (266)
T KOG4024|consen 66 HTELQQALVRFLEAEIQLERKNQKGK-TAPKTFAGFQVT---LKGAEVRLTKKNG-SEKILVVFNVNHSVDMDEGFEDEP 140 (266)
T ss_pred chHHHHHHHHHHHHHHHHHHHhhcCC-ccCccccceEEE---ecCceeEEeeccC-CceEEEEEecCCccCcccCCccCc
Confidence 89999999999999999999887653 467789999997 3457999999999 79999999985 22 222221
Q ss_pred --------CCCcceeeEEEEEcCCCCceEEEEeeecccccCCCce--EEeeEEEecC---CC-CCCCCCccCCCCCCCCH
Q 028909 88 --------RFPREVLMKVCLTKPVLCSILQFDCRVTEKHIEGSDF--DIRNAYYLQS---ST-CLGRPLYRGPMFSSLDP 153 (202)
Q Consensus 88 --------~~~~~~~~~V~I~K~~~~~~L~f~C~~~~~~~~~~~~--~I~~v~~~~~---~~-~~~~~~Y~GP~f~~LDe 153 (202)
+..+.++|+|.|.|++ ++|+|+|++.+++.++++| .|..++.... +. ......|.- .-+.||+
T Consensus 141 sq~~~~~pe~tS~P~F~VeiiKG~--~~L~f~c~~~~~e~QedEy~~~~~~~~~a~f~~~gn~~~~d~vYa~-~gd~lD~ 217 (266)
T KOG4024|consen 141 SQAVAPVPEATSMPPFTVEIIKGD--QRLCFHCELVPVEDQEDEYDFRVEEFYVAPFAKNGNEDVPDEVYAS-SGDYLDP 217 (266)
T ss_pred cccCCCCcccccCCCeEEEEEeCC--eeEEEEeecCCcccCcccccceeeeEEeeecccCCCccCCcceeec-cCcccCH
Confidence 2223578999999976 8999999999877766633 3333332222 21 123456763 5689999
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 028909 154 QLQVALKEYLVARGIGEHLTNYLLLHLHKKEQDQYVNWLQKLESMVAKS 202 (202)
Q Consensus 154 ~Lq~~~~~yLeeRGId~ela~fl~~y~~~KE~~eYi~WL~~vk~Fv~~~ 202 (202)
.|++.|+.||++||||++||.-|.+|++..||.+||.+|++||+|+++.
T Consensus 218 ~LyDlL~~~LeerG~d~~Fa~~Lv~laTa~EH~~YIglLeklkkF~~~q 266 (266)
T KOG4024|consen 218 DLYDLLFVYLEERGLDARFAKTLVALATAYEHSQYIGLLEKLKKFISKQ 266 (266)
T ss_pred HHHHHHHHHHHHcCccHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhcCC
Confidence 9999999999999999999999999999999999999999999999873
No 4
>TIGR01881 cas_Cmr5 CRISPR-associated protein, Cmr5 family. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family, represented by TM1791.1 of Thermotoga maritima, is found in both archaeal and bacterial species as part of the 6-gene CRISPR RAMP module.
Probab=80.64 E-value=6.3 Score=30.36 Aligned_cols=43 Identities=21% Similarity=0.369 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHcCCCHH---HHHHHH-----HHH-HHHHHHHHHHHHHHHH
Q 028909 154 QLQVALKEYLVARGIGEH---LTNYLL-----LHL-HKKEQDQYVNWLQKLE 196 (202)
Q Consensus 154 ~Lq~~~~~yLeeRGId~e---la~fl~-----~y~-~~KE~~eYi~WL~~vk 196 (202)
-|...+..||.++|+-+. +...|. .|+ ...|=-+|+.||+++.
T Consensus 70 ~l~~~l~~~L~~~~~~~~~~~l~~~il~~~~~~y~~~T~eaL~~l~WLKRfA 121 (127)
T TIGR01881 70 KYYAHILYWLKERELVDKFKNALKELMEKDYSDSRIATEEALRYLNWLKRLA 121 (127)
T ss_pred HHHHHHHHHHHHcccccchHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHH
Confidence 578899999999986554 333322 233 4557778999998864
No 5
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=73.21 E-value=7 Score=21.75 Aligned_cols=25 Identities=24% Similarity=0.409 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHH
Q 028909 153 PQLQVALKEYLVARGIGEHLTNYLL 177 (202)
Q Consensus 153 e~Lq~~~~~yLeeRGId~ela~fl~ 177 (202)
++|...+++||.++|-......|..
T Consensus 1 ~~Ln~lI~~YL~~~Gy~~tA~~f~~ 25 (27)
T PF08513_consen 1 EELNQLIYDYLVENGYKETAKAFAK 25 (27)
T ss_dssp HHHHHHHHHHHHHCT-HHHHHHHHH
T ss_pred CHHHHHHHHHHHHCCcHHHHHHHHh
Confidence 4678899999999999988877754
No 6
>PF00123 Hormone_2: Peptide hormone; InterPro: IPR000532 A number of polypeptidic hormones, mainly expressed in the intestine or the pancreas, belong to a group of structurally related peptides [, ]. Once such hormone, glucagon is widely distributed and produced in the alpha-cells of pancreatic islets []. It affects glucose metabolism in the liver [] by inhibiting glycogen synthesis, stimulating glycogenolysis and enchancing gluconeogenesis. It also increases mobilisation of glucose, free fatty acids and ketone bodies, which are metabolites produced in excess in diabetes mellitus. Glucagon is produced, like other peptide hormones, as part of a larger precursor (preproglucagon), which is cleaved to produce glucagon, glucagon-like protein I and glucagon-like protein II []. The structure of glucagon itself is fully conserved in all known mammalian species []. Other members of the structurally similar group include glicentin precursor, secretin, gastric inhibitory protein, vasoactive intestinal peptide (VIP), prealbumin, peptide HI-27 and growth hormone releasing factor.; GO: 0005179 hormone activity, 0005576 extracellular region; PDB: 1T5Q_A 2OBU_A 2QKH_B 2L70_A 2L71_A 2B4N_A 1GCN_A 1D0R_A 3IOL_B 2RRI_A ....
Probab=67.64 E-value=12 Score=21.24 Aligned_cols=24 Identities=17% Similarity=0.355 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 028909 170 EHLTNYLLLHLHKKEQDQYVNWLQ 193 (202)
Q Consensus 170 ~ela~fl~~y~~~KE~~eYi~WL~ 193 (202)
..|.+-...|....--++|++||-
T Consensus 4 g~ftsdys~~L~~~aak~fl~~L~ 27 (28)
T PF00123_consen 4 GTFTSDYSKYLDQLAAKKFLQWLM 27 (28)
T ss_dssp TTHHHHHHHHHHHHHHHHHHHHHC
T ss_pred ccccHHHHHHHHHHHHHHHHHHHh
Confidence 346666677777778899999984
No 7
>KOG4233 consensus DNA-bridging protein BAF [Chromatin structure and dynamics; Replication, recombination and repair]
Probab=63.91 E-value=11 Score=26.84 Aligned_cols=36 Identities=25% Similarity=0.371 Sum_probs=27.7
Q ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028909 160 KEYLVARGIGEHLTNYLLLHLHKKEQDQYVNWLQKL 195 (202)
Q Consensus 160 ~~yLeeRGId~ela~fl~~y~~~KE~~eYi~WL~~v 195 (202)
-.=|.++|+|-.-.-+=.-+...|...++..||+..
T Consensus 32 g~~L~~~GfdkAYvllGQfLllkKdE~lF~~Wlk~~ 67 (90)
T KOG4233|consen 32 GIKLVDAGFDKAYVLLGQFLLLKKDEDLFQEWLKET 67 (90)
T ss_pred hhhHHhccccHHHHHHHHHHHhcccHHHHHHHHHHH
Confidence 445889999987655555556789999999999864
No 8
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=55.46 E-value=12 Score=25.01 Aligned_cols=31 Identities=23% Similarity=0.457 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHHHHHHH-------cCCCHHHHHHHHHH
Q 028909 149 SSLDPQLQVALKEYLVA-------RGIGEHLTNYLLLH 179 (202)
Q Consensus 149 ~~LDe~Lq~~~~~yLee-------RGId~ela~fl~~y 179 (202)
.++++.|++++..||+. |=+.+.|+.||.+-
T Consensus 4 aeiPe~L~~~m~~fie~hP~WDQ~Rl~~aALa~FL~Qn 41 (57)
T PF10929_consen 4 AEIPEDLHQAMKDFIETHPNWDQYRLFQAALAGFLLQN 41 (57)
T ss_pred ccccHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHc
Confidence 47899999999999985 66778888888764
No 9
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=52.39 E-value=24 Score=26.77 Aligned_cols=54 Identities=17% Similarity=0.204 Sum_probs=37.4
Q ss_pred CceEEeeEEEecCCCCCCCCCccCCCCCCCCHHHHHHHHHHHHHcCCCHHHHHHH
Q 028909 122 SDFDIRNAYYLQSSTCLGRPLYRGPMFSSLDPQLQVALKEYLVARGIGEHLTNYL 176 (202)
Q Consensus 122 ~~~~I~~v~~~~~~~~~~~~~Y~GP~f~~LDe~Lq~~~~~yLeeRGId~ela~fl 176 (202)
+.+.|..+.--.-++ .-.+.|.-|.|..|+++-++-+..|+..||==.+++..+
T Consensus 6 ~~l~vt~l~C~~C~t-~i~G~F~l~~~~~L~~E~~~Fi~~Fi~~rGnlKe~e~~l 59 (113)
T PF09862_consen 6 GELVVTRLKCPSCGT-EIEGEFELPWFARLSPEQLEFIKLFIKNRGNLKEMEKEL 59 (113)
T ss_pred CceEEEEEEcCCCCC-EEEeeeccchhhcCCHHHHHHHHHHHHhcCCHHHHHHHH
Confidence 345555554333322 223567778999999999999999999999666665544
No 10
>PRK11814 cysteine desulfurase activator complex subunit SufB; Provisional
Probab=52.14 E-value=29 Score=32.59 Aligned_cols=51 Identities=22% Similarity=0.135 Sum_probs=38.4
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHH-----HHHHHHHHHHHH
Q 028909 143 YRGPMFSSLDPQLQVALKEYLVARGIGEHLTNYLLLHLHKKEQ-----DQYVNWLQKLES 197 (202)
Q Consensus 143 Y~GP~f~~LDe~Lq~~~~~yLeeRGId~ela~fl~~y~~~KE~-----~eYi~WL~~vk~ 197 (202)
=+|.-...||++- .-||.+|||+.+-|.-|.-+..-.|- .++++|+++|=+
T Consensus 423 sHgATvG~ideeq----LFYL~SRGi~e~eA~~Llv~gF~~evi~~ip~e~~~e~~~~i~ 478 (486)
T PRK11814 423 EHEATTSKISEDQ----LFYCRQRGISEEDAVSMIVNGFCKEVFQELPMEFAVEAQKLLA 478 (486)
T ss_pred EeeeecCCCCHHH----HHHHHHcCCCHHHHHHHHHHHHHHHHHHHCCcHHHHHHHHHHH
Confidence 3444556788763 57999999999999988877766663 488999887643
No 11
>smart00070 GLUCA Glucagon like hormones.
Probab=52.06 E-value=23 Score=19.93 Aligned_cols=22 Identities=18% Similarity=0.415 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 028909 171 HLTNYLLLHLHKKEQDQYVNWL 192 (202)
Q Consensus 171 ela~fl~~y~~~KE~~eYi~WL 192 (202)
.|.+-...|....--+.|++||
T Consensus 5 ~ftsdysk~L~~~~ar~fl~~L 26 (27)
T smart00070 5 TFTSDYSKYLDQLAAKKFLQWL 26 (27)
T ss_pred cccHHHHHHHHHHHHHHHHHHh
Confidence 3445555666666678899998
No 12
>PRK13031 preprotein translocase subunit SecB; Provisional
Probab=50.77 E-value=37 Score=26.98 Aligned_cols=71 Identities=13% Similarity=0.312 Sum_probs=40.8
Q ss_pred CCceEeecCCCCceEEEEeecCCCceEEEEEeeCCCCCCCCCCCCcceeeEEEEE-cCCCCceEEEEeeecccccCCCce
Q 028909 46 GDFKVEYDAPQSHDVVLRTKFESGEEVAVSALLGPETFVRESRFPREVLMKVCLT-KPVLCSILQFDCRVTEKHIEGSDF 124 (202)
Q Consensus 46 ~~F~i~~d~~g~~~v~L~r~~~~~E~I~V~~~~~~~~~~ed~~~~~~~~~~V~I~-K~~~~~~L~f~C~~~~~~~~~~~~ 124 (202)
++.+++ .|+...|-.. +.. =+|.|.++++.-..++|+.+. +.++|+++ |.+ ....|-|... ..|.|
T Consensus 17 KDlSFE--~PnaP~if~~-~~~--P~i~v~ln~~a~~l~~e~~yE--V~L~vtvta~~~--~~t~FlvEv~----qaGIF 83 (149)
T PRK13031 17 KDLSFS--IPNSDKIWTT-NWK--PELHTDLKVEATKLPEENTYE--TVLTLEVKVEND--GMVAFEAEVK----QAGIF 83 (149)
T ss_pred eeeccc--CCCCchhhCc-CCC--CceeEEeccCccccCCCCcEE--EEEEEEEEEEeC--CceEEEEEEe----EeeEE
Confidence 555554 6776665544 544 368888877654432233333 44555554 323 2345888874 45779
Q ss_pred EEeeE
Q 028909 125 DIRNA 129 (202)
Q Consensus 125 ~I~~v 129 (202)
.|.++
T Consensus 84 ~i~ni 88 (149)
T PRK13031 84 TVANM 88 (149)
T ss_pred EEcCC
Confidence 88877
No 13
>PF02961 BAF: Barrier to autointegration factor; InterPro: IPR004122 Barrier-to-autointegration factor (BAF) is an essential protein that is highly conserved in metazoan evolution, and which may act as a DNA-bridging protein []. BAF binds directly to double-stranded DNA, to transcription activators, and to inner nuclear membrane proteins, including lamin A filament proteins that anchor nuclear-pore complexes in place, and nuclear LEM-domain proteins that bind to laminins filaments and chromatin. New findings suggest that BAF has structural roles in nuclear assembly and chromatin organisation, represses gene expression and might interlink chromatin structure, nuclear architecture and gene regulation in metazoans []. BAF can be exploited by retroviruses to act as a host component of pre-integration complexes, which promote the integration of the retroviral DNA into the host chromosome by preventing autointegration of retroviral DNA []. BAF might contribute to the assembly or activity of retroviral pre-integration complexes through direct binding to the retroviral proteins p55 Gag and matrix, as well as to DNA.; GO: 0003677 DNA binding; PDB: 2ODG_A 2BZF_A 2EZX_B 2EZY_B 1QCK_B 1CI4_B 2EZZ_B.
Probab=50.73 E-value=20 Score=26.04 Aligned_cols=37 Identities=24% Similarity=0.443 Sum_probs=23.3
Q ss_pred HHHHHHHHcCCCHHHHHHHHH-HHHHHHHHHHHHHHHHH
Q 028909 158 ALKEYLVARGIGEHLTNYLLL-HLHKKEQDQYVNWLQKL 195 (202)
Q Consensus 158 ~~~~yLeeRGId~ela~fl~~-y~~~KE~~eYi~WL~~v 195 (202)
.+-.=|++.|+|-.-. -|-+ +...|.+..+..||++.
T Consensus 30 ~lg~~L~~~GfdKAy~-vLGqfLll~kde~~F~~WLk~~ 67 (89)
T PF02961_consen 30 VLGKRLEEKGFDKAYV-VLGQFLLLKKDEELFQDWLKDT 67 (89)
T ss_dssp HHHHHHHHTT--BHHH-HHHHHHHTTT-HHHHHHHHHHH
T ss_pred HHHHHHHHCCCcHHHH-HhhhhhhccCcHHHHHHHHHHH
Confidence 4456788999987422 2223 35788899999999985
No 14
>COG1490 Dtd D-Tyr-tRNAtyr deacylase [Translation, ribosomal structure and biogenesis]
Probab=49.20 E-value=30 Score=27.27 Aligned_cols=56 Identities=14% Similarity=0.108 Sum_probs=40.7
Q ss_pred CCCceEEeeEEEecCCCCCCCCCccCCCCCCCCHHHHHHHHHHHHHcCCCHHHHHH
Q 028909 120 EGSDFDIRNAYYLQSSTCLGRPLYRGPMFSSLDPQLQVALKEYLVARGIGEHLTNY 175 (202)
Q Consensus 120 ~~~~~~I~~v~~~~~~~~~~~~~Y~GP~f~~LDe~Lq~~~~~yLeeRGId~ela~f 175 (202)
.+..+.|..++.|.+...-.+..+++..=.+.-+.||+.|.+-|.++|+.-+-+.|
T Consensus 70 ~G~iL~VSQFTL~adt~kG~RPsFs~aa~p~~A~~lYe~f~~~lr~~~~~V~tG~F 125 (145)
T COG1490 70 GGEILVVSQFTLYADTKKGRRPSFSKAAKPDQAEELYEYFVELLRELGIKVETGRF 125 (145)
T ss_pred CCcEEEEEEEEEeecccCCCCCCccccCChHHHHHHHHHHHHHHHhcCCcceeeee
Confidence 44567777788887755445556665445688899999999999999987665544
No 15
>PF13154 DUF3991: Protein of unknown function (DUF3991)
Probab=46.02 E-value=16 Score=25.29 Aligned_cols=17 Identities=29% Similarity=0.622 Sum_probs=14.3
Q ss_pred HHHH-cCCCHHHHHHHHH
Q 028909 162 YLVA-RGIGEHLTNYLLL 178 (202)
Q Consensus 162 yLee-RGId~ela~fl~~ 178 (202)
||.+ |||+.++.+.+++
T Consensus 2 YL~~~RgI~~~~v~~~~~ 19 (77)
T PF13154_consen 2 YLTEERGIDPEIVDAFIN 19 (77)
T ss_pred chhhhcCcCHHHHHHHHH
Confidence 7775 9999999988765
No 16
>PF08275 Toprim_N: DNA primase catalytic core, N-terminal domain; InterPro: IPR013264 This is the N-terminal, catalytic core domain of DNA primases. DNA primase (2.7.7 from EC) is a nucleotidyltransferase which synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork. It can also prime the leading strand and has been implicated in cell division []. ; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A 2AU3_A.
Probab=44.99 E-value=16 Score=27.82 Aligned_cols=17 Identities=29% Similarity=0.520 Sum_probs=12.8
Q ss_pred HHHHHHHHcCCCHHHHH
Q 028909 158 ALKEYLVARGIGEHLTN 174 (202)
Q Consensus 158 ~~~~yLeeRGId~ela~ 174 (202)
.-.+||..|||+.+++.
T Consensus 13 ~a~~YL~~Rgl~~e~i~ 29 (128)
T PF08275_consen 13 EALEYLKKRGLSDETIK 29 (128)
T ss_dssp HHHHHHHHTT--HHHHH
T ss_pred HHHHHHHHcCCCHHHHH
Confidence 46899999999999874
No 17
>PHA01623 hypothetical protein
Probab=43.63 E-value=48 Score=21.73 Aligned_cols=29 Identities=24% Similarity=0.332 Sum_probs=24.1
Q ss_pred CCCHHHHHHHHHHHHHcCCCHHHHHHHHHHH
Q 028909 150 SLDPQLQVALKEYLVARGIGEHLTNYLLLHL 180 (202)
Q Consensus 150 ~LDe~Lq~~~~~yLeeRGId~ela~fl~~y~ 180 (202)
.||++|.+.|..|.+..|++ .+++|.+-.
T Consensus 19 rldeel~~~Ld~y~~~~g~~--rSe~IreAI 47 (56)
T PHA01623 19 YMDKDLKTRLKVYCAKNNLQ--LTQAIEEAI 47 (56)
T ss_pred EeCHHHHHHHHHHHHHcCCC--HHHHHHHHH
Confidence 58999999999999999997 666665544
No 18
>PHA02360 hypothetical protein
Probab=39.14 E-value=33 Score=23.42 Aligned_cols=17 Identities=29% Similarity=0.647 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHcCCC
Q 028909 153 PQLQVALKEYLVARGIG 169 (202)
Q Consensus 153 e~Lq~~~~~yLeeRGId 169 (202)
+.|+..++.|-|++||+
T Consensus 29 PklY~~i~k~YEe~gid 45 (70)
T PHA02360 29 PKLYKKIRKYYEEEGID 45 (70)
T ss_pred HHHHHHHHHHHHHcCCc
Confidence 47999999999999997
No 19
>PF00070 Pyr_redox: Pyridine nucleotide-disulphide oxidoreductase; InterPro: IPR001327 FAD flavoproteins belonging to the family of pyridine nucleotide-disulphide oxidoreductases (glutathione reductase, trypanothione reductase, lipoamide dehydrogenase, mercuric reductase, thioredoxin reductase, alkyl hydroperoxide reductase) share sequence similarity with a number of other flavoprotein oxidoreductases, in particular with ferredoxin-NAD+ reductases involved in oxidative metabolism of a variety of hydrocarbons (rubredoxin reductase, putidaredoxin reductase, terpredoxin reductase, ferredoxin-NAD+ reductase components of benzene 1,2-dioxygenase, toluene 1,2-dioxygenase, chlorobenzene dioxygenase, biphenyl dioxygenase), NADH oxidase and NADH peroxidase [, , ]. Comparison of the crystal structures of human glutathione reductase and Escherichia coli thioredoxin reductase reveals different locations of their active sites, suggesting that the enzymes diverged from an ancestral FAD/NAD(P)H reductase and acquired their disulphide reductase activities independently []. Despite functional similarities, oxidoreductases of this family show no sequence similarity with adrenodoxin reductases [] and flavoprotein pyridine nucleotide cytochrome reductases (FPNCR) []. Assuming that disulphide reductase activity emerged later, during divergent evolution, the family can be referred to as FAD-dependent pyridine nucleotide reductases, FADPNR. To date, 3D structures of glutathione reductase [], thioredoxin reductase [], mercuric reductase [], lipoamide dehydrogenase [], trypanothione reductase [] and NADH peroxidase [] have been solved. The enzymes share similar tertiary structures based on a doubly-wound alpha/beta fold, but the relative orientations of their FAD- and NAD(P)H-binding domains may vary significantly. By contrast with the FPNCR family, the folds of the FAD- and NAD(P)H-binding domains are similar, suggesting that the domains evolved by gene duplication []. This entry describes a small NADH binding domain within a larger FAD binding domain described by IPR023753 from INTERPRO. It is found in both class I and class II oxidoreductases. ; GO: 0016491 oxidoreductase activity, 0050660 flavin adenine dinucleotide binding, 0055114 oxidation-reduction process; PDB: 1ZKQ_A 3DGZ_A 1ZDL_A 2R9Z_B 2RAB_A 2A87_B 1M6I_A 2YVG_A 2GR1_A 2GQW_A ....
Probab=36.63 E-value=37 Score=22.98 Aligned_cols=21 Identities=38% Similarity=0.697 Sum_probs=19.4
Q ss_pred CCCCHHHHHHHHHHHHHcCCC
Q 028909 149 SSLDPQLQVALKEYLVARGIG 169 (202)
Q Consensus 149 ~~LDe~Lq~~~~~yLeeRGId 169 (202)
..+|+++...+.++|+.+||+
T Consensus 36 ~~~~~~~~~~~~~~l~~~gV~ 56 (80)
T PF00070_consen 36 PGFDPDAAKILEEYLRKRGVE 56 (80)
T ss_dssp TTSSHHHHHHHHHHHHHTTEE
T ss_pred hhcCHHHHHHHHHHHHHCCCE
Confidence 489999999999999999986
No 20
>PF13434 K_oxygenase: L-lysine 6-monooxygenase (NADPH-requiring); PDB: 3S61_B 3S5W_B.
Probab=36.59 E-value=23 Score=31.48 Aligned_cols=33 Identities=21% Similarity=0.629 Sum_probs=24.9
Q ss_pred HHHHHHHHcCCCHHHHHHH---HHHHHHHHHHHHHHHHH
Q 028909 158 ALKEYLVARGIGEHLTNYL---LLHLHKKEQDQYVNWLQ 193 (202)
Q Consensus 158 ~~~~yLeeRGId~ela~fl---~~y~~~KE~~eYi~WL~ 193 (202)
+|.+||.++| .|..|+ ..+....|-.+|++|..
T Consensus 70 sflnYL~~~~---rl~~f~~~~~~~p~R~ef~dYl~Wva 105 (341)
T PF13434_consen 70 SFLNYLHEHG---RLYEFYNRGYFFPSRREFNDYLRWVA 105 (341)
T ss_dssp SHHHHHHHTT----HHHHHHH--SS-BHHHHHHHHHHHH
T ss_pred cHHHHHHHcC---ChhhhhhcCCCCCCHHHHHHHHHHHH
Confidence 4899999998 566666 45668899999999974
No 21
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=36.02 E-value=83 Score=21.14 Aligned_cols=34 Identities=24% Similarity=0.413 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 028909 155 LQVALKEYLVARGIGEHLTNYLLLHLHKKEQDQYVNWLQKLESMVA 200 (202)
Q Consensus 155 Lq~~~~~yLeeRGId~ela~fl~~y~~~KE~~eYi~WL~~vk~Fv~ 200 (202)
|-+.|..+|+.+|..... .+.|..||+.+..|++
T Consensus 1 Ll~~f~~~l~~~~~s~~T------------i~~Y~~~l~~f~~~~~ 34 (85)
T PF13495_consen 1 LLEEFLEYLRLKGLSEKT------------IKNYRYHLKRFLRFLG 34 (85)
T ss_dssp -HHHHHHHHHHTT--HHH------------HHHHHHHHHHHHTTSS
T ss_pred CHHHHHHHHHHcCCCHHH------------HHHHHHHHHHHHHHcc
Confidence 446788888888887644 3456666666555554
No 22
>PF07063 DUF1338: Domain of unknown function (DUF1338); InterPro: IPR009770 This domain is found in a variety of bacterial and fungal hypothetical proteins of unknown function. The structure of this domain has been solved by structural genomics. The structure implies a zinc-binding function, so it is a putative metal hydrolase (information derived from TOPSAN for PDB:3iuz).; PDB: 3LHO_A 3IUZ_A 2RJB_C.
Probab=34.47 E-value=78 Score=27.99 Aligned_cols=46 Identities=22% Similarity=0.294 Sum_probs=32.1
Q ss_pred CCCCHHHHHHHHHHHHHcCCCHHHHHHH-----------------------------------HHHHHHHHHHHHHHHHH
Q 028909 149 SSLDPQLQVALKEYLVARGIGEHLTNYL-----------------------------------LLHLHKKEQDQYVNWLQ 193 (202)
Q Consensus 149 ~~LDe~Lq~~~~~yLeeRGId~ela~fl-----------------------------------~~y~~~KE~~eYi~WL~ 193 (202)
+.|++.+|+.+.+||..|.+-...+.-+ .+|..=++.++|..|+-
T Consensus 100 e~ls~~~q~~i~~~l~~r~~~~~~~~~~l~~~~~~~~l~~~~a~~~v~~~~~~~~W~~~~ps~~~Y~~L~~eSe~aAWi~ 179 (302)
T PF07063_consen 100 EELSPELQEIIEKYLSRRDPFSPRPLELLDQAERQGGLSAEQADEFVAEALSGFPWQHRAPSLADYQTLLAESEYAAWIA 179 (302)
T ss_dssp GGSSHHHHHHHHHHHTTS-GCGHHHHHHHHHHHHHSCEBHHHHHHHHHHHGGGCSS-SB-SBHHHHHHHHHH-HHHHHHH
T ss_pred hhcCHHHHHHHHHHHhcccCCCHHHHHHHHHHHHcCCCCHHHHHHHHHHHHcccCCCCCCCCHHHHHHHHHHhHHHHhhc
Confidence 5788999999999997777664332222 25666678899999986
Q ss_pred H
Q 028909 194 K 194 (202)
Q Consensus 194 ~ 194 (202)
-
T Consensus 180 ~ 180 (302)
T PF07063_consen 180 A 180 (302)
T ss_dssp H
T ss_pred c
Confidence 5
No 23
>PF14265 DUF4355: Domain of unknown function (DUF4355)
Probab=33.77 E-value=96 Score=23.12 Aligned_cols=40 Identities=25% Similarity=0.419 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028909 154 QLQVALKEYLVARGIGEHLTNYLLLHLHKKEQDQYVNWLQK 194 (202)
Q Consensus 154 ~Lq~~~~~yLeeRGId~ela~fl~~y~~~KE~~eYi~WL~~ 194 (202)
++.......|.+.|++.+|+++|. ..+..+-...+..|..
T Consensus 69 e~~~~~~~~l~e~GLp~~l~~~l~-g~d~e~~~~~v~~l~~ 108 (125)
T PF14265_consen 69 ELRSEAKKVLAEKGLPAELADFLV-GDDEEETKANVKALKK 108 (125)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 455667889999999999999995 4444444444444443
No 24
>smart00777 Mad3_BUB1_I Mad3/BUB1 hoMad3/BUB1 homology region 1. Proteins containing this domain are checkpoint proteins involved in cell division. This region has been shown to be essential for the binding of the binding of BUB1 and MAD3 to CDC20p.
Probab=31.78 E-value=80 Score=24.19 Aligned_cols=30 Identities=23% Similarity=0.325 Sum_probs=26.2
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHHH
Q 028909 157 VALKEYLVARGIGEHLTNYLLLHLHKKEQD 186 (202)
Q Consensus 157 ~~~~~yLeeRGId~ela~fl~~y~~~KE~~ 186 (202)
..+..||..+||...+|.|=..|+..-|.+
T Consensus 83 ~~if~~L~~~~IG~~~AlfYe~~A~~lE~~ 112 (125)
T smart00777 83 RELFQFLYSKGIGTKLALFYEEWAQLLEAA 112 (125)
T ss_pred HHHHHHHHHCCcchhhHHHHHHHHHHHHHc
Confidence 557999999999999999999888877754
No 25
>TIGR02793 nikR nickel-responsive transcriptional regulator NikR. Three members of the seed for this model, from Escherichia coli, Pseudomonas putida, and Brucella melitensis, are found associated with a nickel ABC transporter operon that acts to import nickel for use as a cofactor in urease or hydrogenase. These proteins, with characterized nickel-binding and DNA-binding domains, act as nickel-responsive transcriptional regulators. In the larger family of full-length homologs, most others both lack proximity to the nickel ABC transporter operon and form a separate clade. Several of the homologs not within the scope of this model, but rather scoring between the trusted and noise cutoffs, have been shown to bind nickel, copper, or both, and to regulate genes in response to nickel.
Probab=31.58 E-value=1.2e+02 Score=23.31 Aligned_cols=20 Identities=30% Similarity=0.473 Sum_probs=18.6
Q ss_pred CCCHHHHHHHHHHHHHcCCC
Q 028909 150 SLDPQLQVALKEYLVARGIG 169 (202)
Q Consensus 150 ~LDe~Lq~~~~~yLeeRGId 169 (202)
.||++|.+.|.++.+++|.+
T Consensus 6 slp~~ll~~lD~~~~~~g~~ 25 (129)
T TIGR02793 6 TLDDDLLETLDRLIARRGYQ 25 (129)
T ss_pred EcCHHHHHHHHHHHHHcCCC
Confidence 48999999999999999986
No 26
>smart00667 LisH Lissencephaly type-1-like homology motif. Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.
Probab=30.73 E-value=75 Score=17.19 Aligned_cols=27 Identities=22% Similarity=0.273 Sum_probs=21.3
Q ss_pred CHHHHHHHHHHHHHcCCCHHHHHHHHH
Q 028909 152 DPQLQVALKEYLVARGIGEHLTNYLLL 178 (202)
Q Consensus 152 De~Lq~~~~~yLeeRGId~ela~fl~~ 178 (202)
...|...+.+||...|-......|..+
T Consensus 3 ~~~l~~lI~~yL~~~g~~~ta~~l~~e 29 (34)
T smart00667 3 RSELNRLILEYLLRNGYEETAETLQKE 29 (34)
T ss_pred HHHHHHHHHHHHHHcCHHHHHHHHHHH
Confidence 356788999999999998888766543
No 27
>PF12122 DUF3582: Protein of unknown function (DUF3582); InterPro: IPR022732 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents the N-terminal domain of membrane-bound serine endopeptidases belonging to MEROPS peptidase family S54 (rhomboid-1, clan ST). This domain contains a conserved ASW sequence motif and a single completely conserved residue F that may be functionally important. The tertiary structure of the GlpG protein from Escherichia coli has been determined []. The GlpG protein has six transmembrane domains (other members of the family are predicted to have seven), with the N- and C-terminal ends anchored in the cytoplasm. One transmembrane domain is shorter than the rest, creating an internal, aqueous cavity just below the membrane surface and it is here were proteolysis occurs. There is also a membrane-embedded loop between the first and second transmembrane domains which is postulated to act as a gate controlling substrate access to the active site. No other family of serine peptidases is known to have active site residues within transmembrane domains (although transmembrane active sites are known for aspartic peptidase and metallopeptidases), and the GlpG protein has the type structure for clan ST.; GO: 0004252 serine-type endopeptidase activity, 0016021 integral to membrane; PDB: 3UBB_A 3B45_A 3B44_A 2NRF_A 3TXT_A 2O7L_A 2XTU_A 2IRV_A 2XOW_A 2XTV_A ....
Probab=28.99 E-value=54 Score=24.19 Aligned_cols=22 Identities=27% Similarity=0.588 Sum_probs=16.1
Q ss_pred CHHHHHHHHHHHHHcCCCHHHH
Q 028909 152 DPQLQVALKEYLVARGIGEHLT 173 (202)
Q Consensus 152 De~Lq~~~~~yLeeRGId~ela 173 (202)
++.+-.+|.+||..+||+-.+-
T Consensus 9 n~r~AqaF~DYl~sqgI~~~i~ 30 (101)
T PF12122_consen 9 NPRAAQAFIDYLASQGIELQIE 30 (101)
T ss_dssp SHHHHHHHHHHHHHTT--EEEE
T ss_pred CHHHHHHHHHHHHHCCCeEEEE
Confidence 4578889999999999986543
No 28
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=28.74 E-value=1e+02 Score=19.77 Aligned_cols=30 Identities=23% Similarity=0.223 Sum_probs=24.9
Q ss_pred CCCHHHHHHHHHHHHHcCCCHHHHHHHHHH
Q 028909 150 SLDPQLQVALKEYLVARGIGEHLTNYLLLH 179 (202)
Q Consensus 150 ~LDe~Lq~~~~~yLeeRGId~ela~fl~~y 179 (202)
.|--.|++++.+...+.-|++.+|..|..-
T Consensus 10 tlG~aL~dtLDeli~~~~I~p~La~kVL~~ 39 (49)
T PF02268_consen 10 TLGIALTDTLDELIQEGKITPQLAMKVLEQ 39 (49)
T ss_dssp HHHHHHHHHHHHHHHTTSS-HHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence 455689999999999999999999988653
No 29
>PF10915 DUF2709: Protein of unknown function (DUF2709); InterPro: IPR024484 Members of this family appear restricted to Chlamydiales. Their function is unknown.
Probab=28.22 E-value=91 Score=26.08 Aligned_cols=39 Identities=10% Similarity=0.400 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHH-HHHH
Q 028909 155 LQVALKEYLVARGIGEHLTNYLLLHLHKKEQDQYV-NWLQ 193 (202)
Q Consensus 155 Lq~~~~~yLeeRGId~ela~fl~~y~~~KE~~eYi-~WL~ 193 (202)
+-++|.++|...=+.+..|.|+...+.+-+-.-|+ +|+.
T Consensus 196 iE~~FL~~iq~~L~edKIa~Fve~la~~~~F~~~v~~Wve 235 (238)
T PF10915_consen 196 IEDSFLSFIQDQLVEDKIAEFVESLAEDTEFHPYVEQWVE 235 (238)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHhhc
Confidence 45678888888878889999999999888887776 4654
No 30
>PF08321 PPP5: PPP5 TPR repeat region; InterPro: IPR013235 This domain is specific to the PPP5 subfamily of serine/threonine phosphatases.; GO: 0004722 protein serine/threonine phosphatase activity, 0046872 metal ion binding; PDB: 3ICF_B 3H60_B 3H63_A 3H66_A 3H62_B 1A17_A 1S95_B 3H69_A 3H68_D 3H64_D ....
Probab=27.73 E-value=47 Score=24.19 Aligned_cols=10 Identities=30% Similarity=0.660 Sum_probs=4.0
Q ss_pred CCCccCCCCC
Q 028909 140 RPLYRGPMFS 149 (202)
Q Consensus 140 ~~~Y~GP~f~ 149 (202)
...|.||.++
T Consensus 39 e~sY~GP~l~ 48 (95)
T PF08321_consen 39 EDSYDGPRLE 48 (95)
T ss_dssp -SS--SS--B
T ss_pred CCCCCCCCCC
Confidence 4679999876
No 31
>PRK04460 nickel responsive regulator; Provisional
Probab=27.08 E-value=1.6e+02 Score=22.93 Aligned_cols=20 Identities=30% Similarity=0.449 Sum_probs=18.4
Q ss_pred CCCHHHHHHHHHHHHHcCCC
Q 028909 150 SLDPQLQVALKEYLVARGIG 169 (202)
Q Consensus 150 ~LDe~Lq~~~~~yLeeRGId 169 (202)
.||++|.+.|.++.++||.+
T Consensus 8 slp~~ll~~lD~~~~~~gy~ 27 (137)
T PRK04460 8 SLDSDLLEKFDELIEEKGYQ 27 (137)
T ss_pred EeCHHHHHHHHHHHHHcCCC
Confidence 48999999999999999987
No 32
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=26.97 E-value=42 Score=22.31 Aligned_cols=41 Identities=20% Similarity=0.414 Sum_probs=27.1
Q ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHH
Q 028909 148 FSSLDPQLQVALKEYLVARGIGEHLTNYLLLHLHKKEQDQY 188 (202)
Q Consensus 148 f~~LDe~Lq~~~~~yLeeRGId~ela~fl~~y~~~KE~~eY 188 (202)
|.+|+.=+...+.+...--||.+..|+-|.+|..+.++++-
T Consensus 23 f~sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff~~~~n~~~ 63 (64)
T PF12826_consen 23 FGSLEALMNASVEELSAIPGIGPKIAQSIYEFFQDPENREL 63 (64)
T ss_dssp CSCHHHHCC--HHHHCTSTT--HHHHHHHHHHHH-HHHHHH
T ss_pred cCCHHHHHHcCHHHHhccCCcCHHHHHHHHHHHCCHHhhhh
Confidence 45554444445556666789999999999999999988764
No 33
>COG4003 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.91 E-value=88 Score=22.63 Aligned_cols=26 Identities=31% Similarity=0.466 Sum_probs=18.8
Q ss_pred HHHHHHHHcC-CCHHHHHHHHHHHHHH
Q 028909 158 ALKEYLVARG-IGEHLTNYLLLHLHKK 183 (202)
Q Consensus 158 ~~~~yLeeRG-Id~ela~fl~~y~~~K 183 (202)
.+.+||+.|| |+.+.|++|..-..+|
T Consensus 52 Eii~yleKrGEi~~E~A~~L~~~~~~k 78 (98)
T COG4003 52 EIINYLEKRGEITPEMAKALRVTLVHK 78 (98)
T ss_pred HHHHHHHHhCCCCHHHHHHHHhhHHHH
Confidence 3468888888 7888888887655544
No 34
>PF13376 OmdA: Bacteriocin-protection, YdeI or OmpD-Associated
Probab=26.12 E-value=1.6e+02 Score=19.36 Aligned_cols=40 Identities=13% Similarity=0.351 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028909 149 SSLDPQLQVALKEYLVARGIGEHLTNYLLLHLHKKEQDQYVNWLQKLE 196 (202)
Q Consensus 149 ~~LDe~Lq~~~~~yLeeRGId~ela~fl~~y~~~KE~~eYi~WL~~vk 196 (202)
-.++++|+.+|.. +.....|-..+. .-.|++|+.|+...|
T Consensus 4 ~~vP~dl~~aL~~-------~p~a~~~f~~l~-~~~rr~~i~wi~~AK 43 (63)
T PF13376_consen 4 VEVPEDLEAALEA-------NPEAKEFFESLT-PSYRREYIRWINSAK 43 (63)
T ss_pred CCCCHHHHHHHHC-------CHHHHHHHHHCC-HHHHHHHHHHHHHcC
Confidence 4677888877764 445555555544 446799999997654
No 35
>PF13034 DUF3895: Protein of unknown function (DUF3895)
Probab=25.42 E-value=1.2e+02 Score=21.39 Aligned_cols=28 Identities=21% Similarity=0.310 Sum_probs=21.4
Q ss_pred CCHHHHHHHHHHHH-HcCCCH-HHHHHHHH
Q 028909 151 LDPQLQVALKEYLV-ARGIGE-HLTNYLLL 178 (202)
Q Consensus 151 LDe~Lq~~~~~yLe-eRGId~-ela~fl~~ 178 (202)
|++..|+.+..|++ +.+|+. ++|++|..
T Consensus 1 L~~~e~~~i~~yi~n~~~Isa~elcE~LI~ 30 (78)
T PF13034_consen 1 LSELEKEFINWYIQNEEEISARELCEYLIE 30 (78)
T ss_pred CCHHHHHHHHHHHhccccccHHHHHHHHHH
Confidence 67788889999998 778875 56776653
No 36
>TIGR01981 sufD FeS assembly protein SufD, group 1. This protein, SufD, forms a cytosolic complex SufBCD. This complex enhances the cysteine desulfurase of SufSE. The system, together with SufA, is believed to act in iron-sulfur cluster formation during oxidative stress. SufB and SufD are homologous. Note that SufC belongs to the family of ABC transporter ATP binding proteins, so this protein, encoded by an adjacent gene, has often been annotated as a transporter component.
Probab=25.01 E-value=82 Score=28.28 Aligned_cols=39 Identities=28% Similarity=0.337 Sum_probs=28.9
Q ss_pred CccCCCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Q 028909 142 LYRGPMFSSLDPQLQVALKEYLVARGIGEHLTNYLLLHLHKKE 184 (202)
Q Consensus 142 ~Y~GP~f~~LDe~Lq~~~~~yLeeRGId~ela~fl~~y~~~KE 184 (202)
+-+|--...||++- .=||.+|||+.+-|.-|.-...-.|
T Consensus 314 ~sHgATvG~ldee~----LFYL~SRGi~~~eA~~llv~gF~~~ 352 (366)
T TIGR01981 314 ASHGATVGQIDDEQ----LFYLRSRGIDEEEARRLLIRGFLGE 352 (366)
T ss_pred EecceeecCCCHHH----HHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 34555667888873 5699999999999988876665443
No 37
>PRK13654 magnesium-protoporphyrin IX monomethyl ester cyclase; Provisional
Probab=24.92 E-value=71 Score=28.83 Aligned_cols=35 Identities=17% Similarity=0.408 Sum_probs=28.2
Q ss_pred CCccCCCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHH
Q 028909 141 PLYRGPMFSSLDPQLQVALKEYLVARGIGEHLTNYLL 177 (202)
Q Consensus 141 ~~Y~GP~f~~LDe~Lq~~~~~yLeeRGId~ela~fl~ 177 (202)
..+.+ ..+.||+++...|.+||+. .+++||.-||.
T Consensus 67 ~ef~~-~~d~l~~e~r~~FidFLer-SctaEFSGflL 101 (355)
T PRK13654 67 EEFDQ-DWDHLDPETRKEFIDFLER-SCTAEFSGFLL 101 (355)
T ss_pred hhhhh-chhhCCHHHHHHHHHHHHH-HhhhhhhhHHH
Confidence 34555 6788999999999999975 68888887764
No 38
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=24.44 E-value=62 Score=22.24 Aligned_cols=16 Identities=38% Similarity=0.351 Sum_probs=11.8
Q ss_pred HHHHHHHHHHcCCCHH
Q 028909 156 QVALKEYLVARGIGEH 171 (202)
Q Consensus 156 q~~~~~yLeeRGId~e 171 (202)
|+.|..+|+++||+-.
T Consensus 22 Q~eL~~~L~~~Gi~vT 37 (70)
T PF01316_consen 22 QEELVELLEEEGIEVT 37 (70)
T ss_dssp HHHHHHHHHHTT-T--
T ss_pred HHHHHHHHHHcCCCcc
Confidence 7889999999999854
No 39
>PRK02967 nickel responsive regulator; Provisional
Probab=23.45 E-value=2.2e+02 Score=22.15 Aligned_cols=20 Identities=30% Similarity=0.469 Sum_probs=18.5
Q ss_pred CCCHHHHHHHHHHHHHcCCC
Q 028909 150 SLDPQLQVALKEYLVARGIG 169 (202)
Q Consensus 150 ~LDe~Lq~~~~~yLeeRGId 169 (202)
.||++|-+.|.++.+++|.+
T Consensus 7 slp~~ll~~lD~~~~~~gy~ 26 (139)
T PRK02967 7 TLDDDLLETLDSLIARRGYQ 26 (139)
T ss_pred EcCHHHHHHHHHHHHHcCCC
Confidence 58999999999999999986
No 40
>PHA01748 hypothetical protein
Probab=23.35 E-value=2.3e+02 Score=18.66 Aligned_cols=20 Identities=20% Similarity=0.499 Sum_probs=18.4
Q ss_pred CCCHHHHHHHHHHHHHcCCC
Q 028909 150 SLDPQLQVALKEYLVARGIG 169 (202)
Q Consensus 150 ~LDe~Lq~~~~~yLeeRGId 169 (202)
.||++|...+..|.+..|++
T Consensus 8 rLp~el~~eld~~a~~~g~~ 27 (60)
T PHA01748 8 KIEEDLLELLDRYAIKHGLN 27 (60)
T ss_pred ECCHHHHHHHHHHHHHhCCC
Confidence 58999999999999999997
No 41
>PF07671 DUF1601: Protein of unknown function (DUF1601); InterPro: IPR011632 This repeat is found in a small number of proteins and is apparently limited to Coxiella burnetii.
Probab=23.14 E-value=1.2e+02 Score=18.34 Aligned_cols=17 Identities=18% Similarity=0.386 Sum_probs=14.8
Q ss_pred HHHHHcCCCHHHHHHHH
Q 028909 161 EYLVARGIGEHLTNYLL 177 (202)
Q Consensus 161 ~yLeeRGId~ela~fl~ 177 (202)
.||+++|.++.|..-|.
T Consensus 6 ~~l~~q~L~~~L~~aV~ 22 (37)
T PF07671_consen 6 RYLEEQRLSDRLLDAVR 22 (37)
T ss_pred hhhhhccchHHHHHHHH
Confidence 58899999999988887
No 42
>PF11985 DUF3486: Protein of unknown function (DUF3486); InterPro: IPR021874 This entry is represented by Bacteriophage Mu, Gp27. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=23.13 E-value=3.9e+02 Score=21.27 Aligned_cols=32 Identities=25% Similarity=0.330 Sum_probs=25.0
Q ss_pred CCCCCHHHHHHHHHHHHHcCCC--HHHHHHHHHH
Q 028909 148 FSSLDPQLQVALKEYLVARGIG--EHLTNYLLLH 179 (202)
Q Consensus 148 f~~LDe~Lq~~~~~yLeeRGId--~ela~fl~~y 179 (202)
.+-||+++++.+...|.++|.+ +.++.|+...
T Consensus 7 Id~LP~eir~~l~~~L~~~~~t~~ei~~~~~~~~ 40 (180)
T PF11985_consen 7 IDLLPPEIREWLDQMLRDGGFTQYEILAEWLEEL 40 (180)
T ss_pred HhhCCHHHHHHHHHHHHhCCCChHHHHHHHHHhh
Confidence 4689999999999999999865 3556665553
No 43
>PF13794 MiaE_2: tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)-like; PDB: 3EZ0_C.
Probab=22.92 E-value=80 Score=25.98 Aligned_cols=45 Identities=16% Similarity=0.293 Sum_probs=31.4
Q ss_pred HHHHHHHHHHcCCCHH--HHHHHHHHHHHHHHHHHHHHHHH-HHHhhh
Q 028909 156 QVALKEYLVARGIGEH--LTNYLLLHLHKKEQDQYVNWLQK-LESMVA 200 (202)
Q Consensus 156 q~~~~~yLeeRGId~e--la~fl~~y~~~KE~~eYi~WL~~-vk~Fv~ 200 (202)
++.+...|.+||+|.. ..-|...+-...++..=-.|++. ||.||.
T Consensus 52 f~~L~~~l~~~G~d~~~am~pf~~~ld~f~~rT~P~dW~E~LvKaYVg 99 (185)
T PF13794_consen 52 FERLEARLAERGVDPEEAMEPFVGALDAFHARTRPSDWLESLVKAYVG 99 (185)
T ss_dssp HHHHHHHHHHTT--HHHHHGGGHHHHHHHHHTT--SSHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHH
Confidence 5678899999999997 66777777777777777788888 455653
No 44
>PF01458 UPF0051: Uncharacterized protein family (UPF0051); InterPro: IPR000825 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents SufB and SufD proteins that form part of the SufBCD complex in the SUF system. No specific functions have been assigned to these proteins.; GO: 0016226 iron-sulfur cluster assembly; PDB: 1VH4_B 2ZU0_A 4DN7_A.
Probab=22.80 E-value=49 Score=27.45 Aligned_cols=34 Identities=24% Similarity=0.419 Sum_probs=22.4
Q ss_pred CCccCCCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHHH
Q 028909 141 PLYRGPMFSSLDPQLQVALKEYLVARGIGEHLTNYLLL 178 (202)
Q Consensus 141 ~~Y~GP~f~~LDe~Lq~~~~~yLeeRGId~ela~fl~~ 178 (202)
.+.+|.-...||++- .=||.+|||+.+=|..|.-
T Consensus 193 ~a~H~AtvG~idee~----LFYL~SRGl~~~eA~~Liv 226 (229)
T PF01458_consen 193 KASHGATVGQIDEEQ----LFYLMSRGLSEEEARKLIV 226 (229)
T ss_dssp EEEEEEEEEES-HHH----HHHHHCTT--HHHHHHHHH
T ss_pred EEEEeeEeecCCHHH----HHHHHHcCCCHHHHHHHHH
Confidence 345555566788773 5699999999999987753
No 45
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=22.27 E-value=73 Score=18.85 Aligned_cols=15 Identities=33% Similarity=0.450 Sum_probs=12.4
Q ss_pred HHHHHHHHHcCCCHH
Q 028909 157 VALKEYLVARGIGEH 171 (202)
Q Consensus 157 ~~~~~yLeeRGId~e 171 (202)
+.|.+||++.||...
T Consensus 7 ~~L~~wL~~~gi~~~ 21 (38)
T PF10281_consen 7 SDLKSWLKSHGIPVP 21 (38)
T ss_pred HHHHHHHHHcCCCCC
Confidence 478999999999754
No 46
>PF08311 Mad3_BUB1_I: Mad3/BUB1 homology region 1; InterPro: IPR013212 Proteins containing this domain are checkpoint proteins involved in cell division. This region has been shown to be essential for the binding of BUB1 and MAD3 to CDC20p [].; PDB: 3ESL_B 4AEZ_I 4A1G_B 2LAH_A 2WVI_A 3SI5_B.
Probab=21.86 E-value=94 Score=23.48 Aligned_cols=30 Identities=20% Similarity=0.303 Sum_probs=26.6
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHHHH
Q 028909 157 VALKEYLVARGIGEHLTNYLLLHLHKKEQD 186 (202)
Q Consensus 157 ~~~~~yLeeRGId~ela~fl~~y~~~KE~~ 186 (202)
..+..||..+||...+|.|=..|+..-|+.
T Consensus 83 ~~if~~l~~~~IG~~~A~fY~~wA~~le~~ 112 (126)
T PF08311_consen 83 REIFKFLYSKGIGTKLALFYEEWAEFLEKR 112 (126)
T ss_dssp HHHHHHHHHHTTSTTBHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHcCccHHHHHHHHHHHHHHHHc
Confidence 467889999999999999999999887765
No 47
>COG3486 IucD Lysine/ornithine N-monooxygenase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=21.27 E-value=72 Score=29.65 Aligned_cols=36 Identities=25% Similarity=0.551 Sum_probs=26.9
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 028909 158 ALKEYLVARGIGEHLTNYLLLHLHKKEQDQYVNWLQ 193 (202)
Q Consensus 158 ~~~~yLeeRGId~ela~fl~~y~~~KE~~eYi~WL~ 193 (202)
+|.+||.+-|==-+|-++=.-+...+|-..|++|-.
T Consensus 73 SFLNYL~~h~RLy~Fl~~e~f~i~R~Ey~dY~~Waa 108 (436)
T COG3486 73 SFLNYLHEHGRLYEFLNYETFHIPRREYNDYCQWAA 108 (436)
T ss_pred HHHHHHHHcchHhhhhhhhcccccHHHHHHHHHHHH
Confidence 689999999833334444456777899999999964
No 48
>CHL00185 ycf59 magnesium-protoporphyrin IX monomethyl ester cyclase; Provisional
Probab=21.25 E-value=85 Score=28.27 Aligned_cols=34 Identities=21% Similarity=0.400 Sum_probs=27.5
Q ss_pred CccCCCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHH
Q 028909 142 LYRGPMFSSLDPQLQVALKEYLVARGIGEHLTNYLL 177 (202)
Q Consensus 142 ~Y~GP~f~~LDe~Lq~~~~~yLeeRGId~ela~fl~ 177 (202)
.+.+ ..+.||+++...|.+||+. .+++||.-||.
T Consensus 64 eF~~-~~d~l~~e~r~~FidFLer-ScTaEFSGflL 97 (351)
T CHL00185 64 EFNQ-SWSNLDEKTKSLFVEFLER-SCTAEFSGFLL 97 (351)
T ss_pred hhhh-chhhCCHHHHHHHHHHHHH-HhhhhhhhhHH
Confidence 3444 6788999999999999975 68888887764
No 49
>TIGR02029 AcsF magnesium-protoporphyrin IX monomethyl ester aerobic oxidative cyclase. This model respresents the oxidative cyclase responsible for forming the distinctive E-ring of the chlorin ring system under aerobic conditions. This enzyme is believed to utilize a binuclear iron center and molecular oxygen. There are two isoforms of this enzyme in some plants and cyanobacterai which are differentially regulated based on the levels of copper and oxygen. This step is essential in the biosynthesis of both bacteriochlorophyll and chlorophyll under aerobic conditions (a separate enzyme, BchE, acts under anaerobic conditions). This enzyme is found in plants, cyanobacteria and other photosynthetic bacteria.
Probab=20.66 E-value=87 Score=28.06 Aligned_cols=30 Identities=23% Similarity=0.469 Sum_probs=25.2
Q ss_pred CCCCCCHHHHHHHHHHHHHcCCCHHHHHHHH
Q 028909 147 MFSSLDPQLQVALKEYLVARGIGEHLTNYLL 177 (202)
Q Consensus 147 ~f~~LDe~Lq~~~~~yLeeRGId~ela~fl~ 177 (202)
..++||+++...|.+||+. .+++||.-||.
T Consensus 62 ~~~~l~~e~r~~FidFLer-ScTaEFSGflL 91 (337)
T TIGR02029 62 SWEHIDGELRQAFIEFLER-SCTSEFSGFLL 91 (337)
T ss_pred chhhCCHHHHHHHHHHHHH-HhhhhhhhhHH
Confidence 4567999999999999975 68888887764
No 50
>PF08812 YtxC: YtxC-like family; InterPro: IPR014199 This uncharacterised protein is one of a number of proteins conserved in all known endospore-forming Firmicutes (low-GC Gram-positive bacteria), including Carboxydothermus hydrogenoformans, and it is not found in non-endospore forming species. It is uniformly distributed in the mother cell cytoplasm in Bacillus subtilis [].
Probab=20.52 E-value=1.7e+02 Score=24.45 Aligned_cols=26 Identities=19% Similarity=0.259 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 028909 172 LTNYLLLHLHKKEQDQYVNWLQKLESMVA 200 (202)
Q Consensus 172 la~fl~~y~~~KE~~eYi~WL~~vk~Fv~ 200 (202)
.-..+.+|+..||.+|+++. ||.||.
T Consensus 105 ve~aVdEy~~EkEY~eFI~l---LryFV~ 130 (221)
T PF08812_consen 105 VEKAVDEYLMEKEYQEFIQL---LRYFVD 130 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHH---HHHHHH
Confidence 33456677777775555554 566664
No 51
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=20.48 E-value=2.7e+02 Score=18.38 Aligned_cols=34 Identities=24% Similarity=0.130 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 028909 150 SLDPQLQVALKEYLVARGIGEHLTNYLLLHLHKK 183 (202)
Q Consensus 150 ~LDe~Lq~~~~~yLeeRGId~ela~fl~~y~~~K 183 (202)
.|...-.+.+..+++.-|.+.++......|+..+
T Consensus 12 ~ls~~e~~~i~~~~~~~~~~~evI~~ai~~a~~~ 45 (73)
T TIGR01446 12 MLSPFEMEDLKYWLDEFGNSPELIKEALKEAVSN 45 (73)
T ss_pred CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHc
Confidence 5778888999999999999999999999998764
No 52
>PF09701 Cas_Cmr5: CRISPR-associated protein (Cas_Cmr5); InterPro: IPR010160 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a family of Cas proteins as represented by TM1791.1 from Thermotoga maritima. This family of Cas proteins are found in both archaeal and bacterial species.; PDB: 2OEB_A 2ZOP_A.
Probab=20.46 E-value=1.5e+02 Score=22.21 Aligned_cols=41 Identities=24% Similarity=0.425 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHcCCCH-----HHHHHHHH-----HH-HHHHHHHHHHHHHHH
Q 028909 155 LQVALKEYLVARGIGE-----HLTNYLLL-----HL-HKKEQDQYVNWLQKL 195 (202)
Q Consensus 155 Lq~~~~~yLeeRGId~-----ela~fl~~-----y~-~~KE~~eYi~WL~~v 195 (202)
|.+.+..||..++... +|...|.. |+ ...|=-++..||++.
T Consensus 66 l~~~l~~wl~~~~~~~~~~~~~l~~~i~~~d~~~Y~~~t~e~La~l~WlKRf 117 (122)
T PF09701_consen 66 LLEHLAEWLCERFKIDPNENNDLLEAIIEADLSEYMRATREALAFLNWLKRF 117 (122)
T ss_dssp HHHHHHHHCCHTTHCTSS---HHHHHHHHS-HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhccccchhhHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence 8888899998877643 45554432 22 223334566777764
No 53
>PRK10948 cysteine desulfurase activator complex subunit SufD; Provisional
Probab=20.25 E-value=1.2e+02 Score=28.12 Aligned_cols=38 Identities=21% Similarity=0.343 Sum_probs=28.6
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Q 028909 143 YRGPMFSSLDPQLQVALKEYLVARGIGEHLTNYLLLHLHKKE 184 (202)
Q Consensus 143 Y~GP~f~~LDe~Lq~~~~~yLeeRGId~ela~fl~~y~~~KE 184 (202)
=+|--...||++- .=||.+|||+.+-|.-|.-+..-.|
T Consensus 360 sHgATvG~ldee~----LFYL~SRGi~~~~A~~Llv~gF~~e 397 (424)
T PRK10948 360 SHGATVGRIDDEQ----LFYLRSRGINQQDAQQMIIYAFAAE 397 (424)
T ss_pred EeeeecCCCCHHH----HHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 3455567888873 3799999999999988877666554
No 54
>COG0218 Predicted GTPase [General function prediction only]
Probab=20.25 E-value=1.5e+02 Score=24.70 Aligned_cols=37 Identities=19% Similarity=0.338 Sum_probs=24.3
Q ss_pred eEEee-EEEecCCCCCCCCCcc-CCCCCCCCHHHHHHHHHHHHHc
Q 028909 124 FDIRN-AYYLQSSTCLGRPLYR-GPMFSSLDPQLQVALKEYLVAR 166 (202)
Q Consensus 124 ~~I~~-v~~~~~~~~~~~~~Y~-GP~f~~LDe~Lq~~~~~yLeeR 166 (202)
|.|++ +.+++=.+ --|. ||. .+-+..++.+.+||+.|
T Consensus 66 f~~~~~~~lVDlPG----YGyAkv~k--~~~e~w~~~i~~YL~~R 104 (200)
T COG0218 66 FEVDDELRLVDLPG----YGYAKVPK--EVKEKWKKLIEEYLEKR 104 (200)
T ss_pred EEecCcEEEEeCCC----cccccCCH--HHHHHHHHHHHHHHhhc
Confidence 55555 66665432 2233 564 77788888899999998
No 55
>cd06206 bifunctional_CYPOR These bifunctional proteins fuse N-terminal cytochrome p450 with a cytochrome p450 reductase (CYPOR). NADPH cytochrome p450 reductase serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a la
Probab=20.03 E-value=97 Score=27.82 Aligned_cols=41 Identities=10% Similarity=0.011 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHHcCC-CHHHHHHHHHHHHHHHHHHHHHHHH
Q 028909 153 PQLQVALKEYLVARGI-GEHLTNYLLLHLHKKEQDQYVNWLQ 193 (202)
Q Consensus 153 e~Lq~~~~~yLeeRGI-d~ela~fl~~y~~~KE~~eYi~WL~ 193 (202)
=+|++.|..||.-+|+ ...|...|..|+.+.++++-+..+.
T Consensus 79 ~tl~~~l~~~~Di~~~p~~~~l~~la~~~~~~~~k~~l~~~~ 120 (384)
T cd06206 79 ISVSELLSSYVELSQPATRRQLAALAEATRCPDTKALLERLA 120 (384)
T ss_pred EEHHHHHHhhccccCCCCHHHHHHHHHHCCCHHHHHHHHHhh
Confidence 3899999999999999 8999999999998888887665553
No 56
>PF12123 Amidase02_C: N-acetylmuramoyl-l-alanine amidase; InterPro: IPR021976 This domain is found in bacteria and viruses. This domain is about 50 amino acids in length. This domain is classified with the enzyme classification code 3.5.1.28 from EC. This domain is the C-terminal of the enzyme which hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides. ; PDB: 2L48_B.
Probab=20.00 E-value=1.2e+02 Score=19.20 Aligned_cols=20 Identities=20% Similarity=0.228 Sum_probs=13.4
Q ss_pred CCCCHHHHHHHHHHHHHcCC
Q 028909 149 SSLDPQLQVALKEYLVARGI 168 (202)
Q Consensus 149 ~~LDe~Lq~~~~~yLeeRGI 168 (202)
+-+++.--+.+..||.+||.
T Consensus 22 ~~~s~~~L~k~~~wld~rgW 41 (45)
T PF12123_consen 22 DPLSDAELDKFTAWLDERGW 41 (45)
T ss_dssp ----HHHHHHHHHHHHHTT-
T ss_pred CCCCHHHHHHHHHHHHhcCc
Confidence 34666777899999999984
Done!